Package: goseq

Version: 1.32.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:goseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings goseq_1.32.0.tar.gz

StartedAt: 2018-10-17 02:29:42 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 02:36:45 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 422.2 seconds

RetCode: 0

Status:  OK

CheckDir: goseq.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:goseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings goseq_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/goseq.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'goseq/DESCRIPTION' ... OK
* this is package 'goseq' version '1.32.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'goseq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'rtracklayer' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for 'winMenuAddItem'
getgo: no visible global function definition for 'toTable'
getlength: no visible global function definition for
  'installed.packages'
getlength: no visible global function definition for 'tail'
getlength: no visible global function definition for 'toTable'
getlength: no visible global function definition for
  'transcriptLengths'
getlength: no visible global function definition for 'browserSession'
getlength: no visible global function definition for 'genome<-'
getlength: no visible global function definition for 'ucscTableQuery'
getlength: no visible global function definition for 'getTable'
makespline: no visible global function definition for 'show'
supportedOrganisms: no visible global function definition for
  'ucscGenomes'
Undefined global functions or variables:
  browserSession genome<- getTable installed.packages show tail toTable
  transcriptLengths ucscGenomes ucscTableQuery winMenuAddItem
Consider adding
  importFrom("methods", "show")
  importFrom("utils", "installed.packages", "tail", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
goseq     46.92   2.08   49.19
getgo     13.13   1.08   14.20
nullp      8.37   1.31    9.69
getlength  6.33   1.45    8.37
plotPWF    7.02   0.70    7.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
goseq     31.25   1.34   32.59
getgo     11.62   0.73   12.36
nullp      7.28   0.93    8.20
plotPWF    5.14   0.67    5.81
getlength  4.50   0.72    5.22
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/goseq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/goseq_1.32.0.tar.gz && rm -rf goseq.buildbin-libdir && mkdir goseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=goseq.buildbin-libdir goseq_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL goseq_1.32.0.zip && rm goseq_1.32.0.tar.gz goseq_1.32.0.zip
###
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install for i386

* installing *source* package 'goseq' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'goseq'
    finding HTML links ... done
    genes                                   html  
    getgo                                   html  
    finding level-2 HTML links ... done

    getlength                               html  
    goseq                                   html  
    makespline                              html  
    nullp                                   html  
    plotPWF                                 html  
    supportedOrganisms                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'goseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'goseq' as goseq_1.32.0.zip
* DONE (goseq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'goseq' successfully unpacked and MD5 sums checked
In R CMD INSTALL